Louis BECQUEY / biorseo

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Louis BECQUEY
1c59c960 1 parent 72060257

some cleaning + temp folder

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Showing 1 changed file with 35 additions and 250 deletions
...@@ -25,6 +25,7 @@ modulespath = biorseoDir + "/data/modules" ...@@ -25,6 +25,7 @@ modulespath = biorseoDir + "/data/modules"
25 HLmotifDir = modulespath + "/BGSU/HL/3.2/lib" 25 HLmotifDir = modulespath + "/BGSU/HL/3.2/lib"
26 ILmotifDir = modulespath + "/BGSU/IL/3.2/lib" 26 ILmotifDir = modulespath + "/BGSU/IL/3.2/lib"
27 descfolder = modulespath + "/DESC" 27 descfolder = modulespath + "/DESC"
28 +tempDir = "temp/"
28 29
29 # Parse options 30 # Parse options
30 try: 31 try:
...@@ -84,12 +85,6 @@ class Loop: ...@@ -84,12 +85,6 @@ class Loop:
84 self.type = looptype 85 self.type = looptype
85 self.position = position 86 self.position = position
86 87
87 - def get_header(self):
88 - return self.header
89 -
90 - def subsequence(self):
91 - return self.seq
92 -
93 88
94 class InsertionSite: 89 class InsertionSite:
95 def __init__(self, loop, csv_line): 90 def __init__(self, loop, csv_line):
...@@ -151,177 +146,6 @@ class RNA: ...@@ -151,177 +146,6 @@ class RNA:
151 self.biorseoBGSUBayesPairD = [] 146 self.biorseoBGSUBayesPairD = []
152 self.biorseoBGSUBayesPairB = [] 147 self.biorseoBGSUBayesPairB = []
153 148
154 - def get_RNAsubopt_results(self):
155 - rna = open(self.outputf + self.basename + ".subopt", "r")
156 - lines = rna.readlines()
157 - rna.close()
158 - for i in range(2, len(lines)):
159 - ss = lines[i].split(' ')[0]
160 - if ss not in self.rnasubopt.predictions:
161 - self.rnasubopt.predictions.append(ss)
162 -
163 - def get_biorseoBayesPairA_results(self, targetdir):
164 - if path.isfile(targetdir+ self.basename + ".bypA"):
165 - rna = open(targetdir+ self.basename + ".bypA", "r")
166 - lines = rna.readlines()
167 - rna.close()
168 - for i in range(2, len(lines)):
169 - ss = lines[i].split(' ')[0].split('\t')[0]
170 - if ss not in self.biorseoBayesPairA.predictions:
171 - self.biorseoBayesPairA.predictions.append(ss)
172 - self.biorseoBayesPairA.ninsertions.append(lines[i].count('+'))
173 -
174 - def get_biorseoBayesPairB_results(self, targetdir):
175 - if path.isfile(targetdir+ self.basename + ".bypB"):
176 - rna = open(targetdir+ self.basename + ".bypB", "r")
177 - lines = rna.readlines()
178 - rna.close()
179 - for i in range(2, len(lines)):
180 - ss = lines[i].split(' ')[0].split('\t')[0]
181 - if ss not in self.biorseoBayesPairB.predictions:
182 - self.biorseoBayesPairB.predictions.append(ss)
183 - self.biorseoBayesPairB.ninsertions.append(lines[i].count('+'))
184 -
185 - def get_biorseoBayesPairC_results(self, targetdir):
186 - if path.isfile(targetdir+ self.basename + ".bypC"):
187 - rna = open(targetdir+ self.basename + ".bypC", "r")
188 - lines = rna.readlines()
189 - rna.close()
190 - for i in range(2, len(lines)):
191 - ss = lines[i].split(' ')[0].split('\t')[0]
192 - if ss not in self.biorseoBayesPairC.predictions:
193 - self.biorseoBayesPairC.predictions.append(ss)
194 - self.biorseoBayesPairC.ninsertions.append(lines[i].count('+'))
195 -
196 - def get_biorseoBayesPairD_results(self, targetdir):
197 - if path.isfile(targetdir+ self.basename + ".bypD"):
198 - rna = open(targetdir+ self.basename + ".bypD", "r")
199 - lines = rna.readlines()
200 - rna.close()
201 - for i in range(2, len(lines)):
202 - ss = lines[i].split(' ')[0].split('\t')[0]
203 - if ss not in self.biorseoBayesPairD.predictions:
204 - self.biorseoBayesPairD.predictions.append(ss)
205 - self.biorseoBayesPairD.ninsertions.append(lines[i].count('+'))
206 -
207 - def get_biorseoRawA_results(self, targetdir):
208 - if path.isfile(targetdir+ self.basename + ".rawA"):
209 - rna = open(targetdir+ self.basename + ".rawA", "r")
210 - lines = rna.readlines()
211 - rna.close()
212 - for i in range(2, len(lines)):
213 - ss = lines[i].split(' ')[0].split('\t')[0]
214 - if ss not in self.biorseoRawA.predictions:
215 - self.biorseoRawA.predictions.append(ss)
216 - self.biorseoRawA.ninsertions.append(lines[i].count('+'))
217 -
218 - def get_biorseoRawB_results(self, targetdir):
219 - if path.isfile(targetdir+ self.basename + ".rawB"):
220 - rna = open(targetdir+ self.basename + ".rawB", "r")
221 - lines = rna.readlines()
222 - rna.close()
223 - for i in range(2, len(lines)):
224 - ss = lines[i].split(' ')[0].split('\t')[0]
225 - if ss not in self.biorseoRawB.predictions:
226 - self.biorseoRawB.predictions.append(ss)
227 - self.biorseoRawB.ninsertions.append(lines[i].count('+'))
228 -
229 - def get_biorseoBGSUJAR3DA_results(self, targetdir):
230 - if path.isfile(targetdir+ self.basename + ".jar3dA"):
231 - rna = open(targetdir+ self.basename + ".jar3dA", "r")
232 - lines = rna.readlines()
233 - rna.close()
234 - for i in range(2, len(lines)):
235 - ss = lines[i].split(' ')[0].split('\t')[0]
236 - if ss not in self.biorseoBGSUJAR3DA.predictions:
237 - self.biorseoBGSUJAR3DA.predictions.append(ss)
238 - self.biorseoBGSUJAR3DA.ninsertions.append(lines[i].count('+'))
239 -
240 - def get_biorseoBGSUJAR3DB_results(self, targetdir):
241 - if path.isfile(targetdir+ self.basename + ".jar3dB"):
242 - rna = open(targetdir+ self.basename + ".jar3dB", "r")
243 - lines = rna.readlines()
244 - rna.close()
245 - for i in range(2, len(lines)):
246 - ss = lines[i].split(' ')[0].split('\t')[0]
247 - if ss not in self.biorseoBGSUJAR3DB.predictions:
248 - self.biorseoBGSUJAR3DB.predictions.append(ss)
249 - self.biorseoBGSUJAR3DB.ninsertions.append(lines[i].count('+'))
250 -
251 - def get_biorseoBGSUJAR3DC_results(self, targetdir):
252 - if path.isfile(targetdir+ self.basename + ".jar3dC"):
253 - rna = open(targetdir+ self.basename + ".jar3dC", "r")
254 - lines = rna.readlines()
255 - rna.close()
256 - for i in range(2, len(lines)):
257 - ss = lines[i].split(' ')[0].split('\t')[0]
258 - if ss not in self.biorseoBGSUJAR3DC.predictions:
259 - self.biorseoBGSUJAR3DC.predictions.append(ss)
260 - self.biorseoBGSUJAR3DC.ninsertions.append(lines[i].count('+'))
261 -
262 - def get_biorseoBGSUJAR3DD_results(self, targetdir):
263 - if path.isfile(targetdir+ self.basename + ".jar3dD"):
264 - rna = open(targetdir+ self.basename + ".jar3dD", "r")
265 - lines = rna.readlines()
266 - rna.close()
267 - for i in range(2, len(lines)):
268 - ss = lines[i].split(' ')[0].split('\t')[0]
269 - if ss not in self.biorseoBGSUJAR3DD.predictions:
270 - self.biorseoBGSUJAR3DD.predictions.append(ss)
271 - self.biorseoBGSUJAR3DD.ninsertions.append(lines[i].count('+'))
272 -
273 - def get_biorseoBGSUBayesPairA_results(self, targetdir):
274 - if path.isfile(targetdir+ self.basename + ".bgsubypA"):
275 - rna = open(targetdir+ self.basename + ".bgsubypA", "r")
276 - lines = rna.readlines()
277 - rna.close()
278 - for i in range(2, len(lines)):
279 - ss = lines[i].split(' ')[0].split('\t')[0]
280 - if ss not in self.biorseoBGSUBayesPairA.predictions:
281 - self.biorseoBGSUBayesPairA.predictions.append(ss)
282 - self.biorseoBGSUBayesPairA.ninsertions.append(lines[i].count('+'))
283 - # else:
284 - # print(targetdir+ self.basename + ".bgsubypA not found !")
285 -
286 - def get_biorseoBGSUBayesPairB_results(self, targetdir):
287 - if path.isfile(targetdir+ self.basename + ".bgsubypB"):
288 - rna = open(targetdir+ self.basename + ".bgsubypB", "r")
289 - lines = rna.readlines()
290 - rna.close()
291 - for i in range(2, len(lines)):
292 - ss = lines[i].split(' ')[0].split('\t')[0]
293 - if ss not in self.biorseoBGSUBayesPairB.predictions:
294 - self.biorseoBGSUBayesPairB.predictions.append(ss)
295 - self.biorseoBGSUBayesPairB.ninsertions.append(lines[i].count('+'))
296 - # else:
297 - # print(targetdir+ self.basename + ".bgsubypB not found !")
298 -
299 - def get_biorseoBGSUBayesPairC_results(self, targetdir):
300 - if path.isfile(targetdir+ self.basename + ".bgsubypC"):
301 - rna = open(targetdir+ self.basename + ".bgsubypC", "r")
302 - lines = rna.readlines()
303 - rna.close()
304 - for i in range(2, len(lines)):
305 - ss = lines[i].split(' ')[0].split('\t')[0]
306 - if ss not in self.biorseoBGSUBayesPairC.predictions:
307 - self.biorseoBGSUBayesPairC.predictions.append(ss)
308 - self.biorseoBGSUBayesPairC.ninsertions.append(lines[i].count('+'))
309 - # else:
310 - # print(targetdir+ self.basename + ".bgsubypC not found !")
311 -
312 - def get_biorseoBGSUBayesPairD_results(self, targetdir):
313 - if path.isfile(targetdir+ self.basename + ".bgsubypD"):
314 - rna = open(targetdir+ self.basename + ".bgsubypD", "r")
315 - lines = rna.readlines()
316 - rna.close()
317 - for i in range(2, len(lines)):
318 - ss = lines[i].split(' ')[0].split('\t')[0]
319 - if ss not in self.biorseoBGSUBayesPairD.predictions:
320 - self.biorseoBGSUBayesPairD.predictions.append(ss)
321 - self.biorseoBGSUBayesPairD.ninsertions.append(lines[i].count('+'))
322 - # else:
323 - # print(targetdir+ self.basename + ".bgsubypD not found !")
324 -
325 149
326 class BiorseoInstance: 150 class BiorseoInstance:
327 def __init__(self, opts): 151 def __init__(self, opts):
...@@ -420,7 +244,9 @@ class BiorseoInstance: ...@@ -420,7 +244,9 @@ class BiorseoInstance:
420 self.list_jobs() 244 self.list_jobs()
421 245
422 # run them 246 # run them
423 - self.execute_jobs() 247 + self.execute_jobs()
248 +
249 + # subprocess.call(["rm", "-rf", tempDir]) # empty the temp folder
424 250
425 def enumerate_loops(self, s): 251 def enumerate_loops(self, s):
426 def resort(unclosedLoops): 252 def resort(unclosedLoops):
...@@ -532,28 +358,29 @@ class BiorseoInstance: ...@@ -532,28 +358,29 @@ class BiorseoInstance:
532 358
533 def launch_JAR3D_worker(self, loop): 359 def launch_JAR3D_worker(self, loop):
534 # write motif to a file 360 # write motif to a file
535 - newpath = getcwd()+'/'+loop.header[1:] 361 + modulefolder = tempDir + loop.header[1:] + '/'
536 - if not path.exists(newpath): 362 + if not path.exists(modulefolder):
537 - makedirs(newpath) 363 + makedirs(modulefolder)
538 - chdir(newpath) 364 + filename = modulefolder + loop.header[1:]+".fasta"
539 - filename = loop.header[1:]+".fasta"
540 fasta = open(filename, 'w') 365 fasta = open(filename, 'w')
541 - fasta.write('>'+loop.get_header()+'\n'+loop.subsequence()+'\n') 366 + fasta.write('>'+loop.header+'\n'+loop.seq+'\n')
542 fasta.close() 367 fasta.close()
543 368
544 # Launch Jar3D on it 369 # Launch Jar3D on it
545 if loop.type == 'h': 370 if loop.type == 'h':
546 - cmd = ["java", "-jar", jar3dexec, filename, HLmotifDir+"/all.txt", 371 + cmd = ["java", "-jar", jar3dexec, loop.header[1:]+".fasta", HLmotifDir+"/all.txt",
547 loop.header[1:]+".HLloop.csv", loop.header[1:]+".HLseq.csv"] 372 loop.header[1:]+".HLloop.csv", loop.header[1:]+".HLseq.csv"]
548 else: 373 else:
549 - cmd = ["java", "-jar", jar3dexec, filename, ILmotifDir+"/all.txt", 374 + cmd = ["java", "-jar", jar3dexec, loop.header[1:]+".fasta", ILmotifDir+"/all.txt",
550 loop.header[1:]+".ILloop.csv", loop.header[1:]+".ILseq.csv"] 375 loop.header[1:]+".ILloop.csv", loop.header[1:]+".ILseq.csv"]
551 nowhere = open(devnull, 'w') 376 nowhere = open(devnull, 'w')
552 logfile = open(biorseoDir + "/log_of_the_run.sh", 'a') 377 logfile = open(biorseoDir + "/log_of_the_run.sh", 'a')
553 logfile.write(' '.join(cmd)) 378 logfile.write(' '.join(cmd))
554 logfile.write("\n") 379 logfile.write("\n")
555 logfile.close() 380 logfile.close()
381 + chdir(modulefolder)
556 subprocess.call(cmd, stdout=nowhere) 382 subprocess.call(cmd, stdout=nowhere)
383 + chdir(biorseoDir)
557 nowhere.close() 384 nowhere.close()
558 385
559 # Retrieve results 386 # Retrieve results
...@@ -562,7 +389,7 @@ class BiorseoInstance: ...@@ -562,7 +389,7 @@ class BiorseoInstance:
562 capstype = "HL" 389 capstype = "HL"
563 else: 390 else:
564 capstype = "IL" 391 capstype = "IL"
565 - csv = open(loop.header[1:]+".%sseq.csv" % capstype, 'r') 392 + csv = open(modulefolder + loop.header[1:] +".%sseq.csv" % capstype, 'r')
566 l = csv.readline() 393 l = csv.readline()
567 while l: 394 while l:
568 if "true" in l: 395 if "true" in l:
...@@ -570,15 +397,12 @@ class BiorseoInstance: ...@@ -570,15 +397,12 @@ class BiorseoInstance:
570 l = csv.readline() 397 l = csv.readline()
571 csv.close() 398 csv.close()
572 399
573 - # Cleaning
574 - chdir("..")
575 - subprocess.call(["rm", "-r", loop.header[1:]])
576 return insertion_sites 400 return insertion_sites
577 401
578 def launch_JAR3D(self, seq_, basename): 402 def launch_JAR3D(self, seq_, basename):
579 rnasubopt_preds = [] 403 rnasubopt_preds = []
580 # Extracting probable loops from RNA-subopt structures 404 # Extracting probable loops from RNA-subopt structures
581 - rna = open(self.outputf + basename + ".subopt", "r") 405 + rna = open(tempDir + basename + ".subopt", "r")
582 lines = rna.readlines() 406 lines = rna.readlines()
583 rna.close() 407 rna.close()
584 for i in range(2, len(lines)): 408 for i in range(2, len(lines)):
...@@ -597,19 +421,16 @@ class BiorseoInstance: ...@@ -597,19 +421,16 @@ class BiorseoInstance:
597 # Retrieve subsequences corresponding to the possible loops 421 # Retrieve subsequences corresponding to the possible loops
598 loops = [] 422 loops = []
599 for i, l in enumerate(HLs): 423 for i, l in enumerate(HLs):
600 - loops.append( 424 + loops.append(Loop(">HL%d" % (i+1), seq_[l[0][0]-1:l[0][1]], "h", l))
601 - Loop(">HL%d" % (i+1), seq_[l[0][0]-1:l[0][1]], "h", l))
602 for i, l in enumerate(ILs): 425 for i, l in enumerate(ILs):
603 - loops.append( 426 + loops.append(Loop(">IL%d" % (i+1), seq_[l[0][0]-1:l[0][1]]+'*'+seq_[l[1][0]-1:l[1][1]], "i", l))
604 - Loop(">IL%d" % (i+1), seq_[l[0][0]-1:l[0][1]]+'*'+seq_[l[1][0]-1:l[1][1]], "i", l))
605 # Scanning loop subsequences against motif database 427 # Scanning loop subsequences against motif database
606 pool = MyPool(processes=cpu_count()) 428 pool = MyPool(processes=cpu_count())
607 - insertion_sites = [x for y in pool.map( 429 + insertion_sites = [x for y in pool.map(self.launch_JAR3D_worker, loops) for x in y]
608 - self.launch_JAR3D_worker, loops) for x in y]
609 insertion_sites.sort(reverse=True) 430 insertion_sites.sort(reverse=True)
610 # Writing results to CSV file 431 # Writing results to CSV file
611 c = 0 432 c = 0
612 - resultsfile = open(self.outputf+basename+".sites.csv", "w") 433 + resultsfile = open(biorseoDir + "/" + tempDir+basename+".sites.csv", "w")
613 resultsfile.write("Motif,Rotation,Score,Start1,End1,Start2,End2\n") 434 resultsfile.write("Motif,Rotation,Score,Start1,End1,Start2,End2\n")
614 for site in insertion_sites: 435 for site in insertion_sites:
615 if site.score > 10: 436 if site.score > 10:
...@@ -617,7 +438,7 @@ class BiorseoInstance: ...@@ -617,7 +438,7 @@ class BiorseoInstance:
617 string = "FOUND with score %d:\t\t possible insertion of motif " % site.score + site.atlas_id 438 string = "FOUND with score %d:\t\t possible insertion of motif " % site.score + site.atlas_id
618 if site.rotation: 439 if site.rotation:
619 string += " (reversed)" 440 string += " (reversed)"
620 - string += (" on " + site.loop.get_header() + " at positions") 441 + string += (" on " + site.loop.header + " at positions")
621 resultsfile.write(site.atlas_id+',' + 442 resultsfile.write(site.atlas_id+',' +
622 str(bool(site.rotation))+",%d" % site.score+',') 443 str(bool(site.rotation))+",%d" % site.score+',')
623 positions = [','.join([str(y) for y in x]) for x in site.position] 444 positions = [','.join([str(y) for y in x]) for x in site.position]
...@@ -629,10 +450,10 @@ class BiorseoInstance: ...@@ -629,10 +450,10 @@ class BiorseoInstance:
629 def launch_BayesPairing(self, module_type, seq_, header_): 450 def launch_BayesPairing(self, module_type, seq_, header_):
630 chdir(bypdir) 451 chdir(bypdir)
631 452
632 - cmd = ["python3", "parse_sequences.py", "-seq", self.outputf + 453 + cmd = ["python3", "parse_sequences.py", "-seq", biorseoDir + '/' + tempDir +
633 header_ + ".fa", "-d", module_type, "-interm", "1"] 454 header_ + ".fa", "-d", module_type, "-interm", "1"]
634 455
635 - logfile = open("log_of_the_run.sh", 'a') 456 + logfile = open(biorseoDir + "/log_of_the_run.sh", 'a')
636 logfile.write(" ".join(cmd)) 457 logfile.write(" ".join(cmd))
637 logfile.write("\n") 458 logfile.write("\n")
638 logfile.close() 459 logfile.close()
...@@ -646,9 +467,9 @@ class BiorseoInstance: ...@@ -646,9 +467,9 @@ class BiorseoInstance:
646 l = BypLog[idx] 467 l = BypLog[idx]
647 insertion_sites = [x for x in ast.literal_eval(l.split(":")[1][1:])] 468 insertion_sites = [x for x in ast.literal_eval(l.split(":")[1][1:])]
648 if module_type == "rna3dmotif": 469 if module_type == "rna3dmotif":
649 - rna = open(self.outputf + header_ + ".byp.csv", "w") 470 + rna = open(biorseoDir + "/" + tempDir + header_ + ".byp.csv", "w")
650 else: 471 else:
651 - rna = open(self.outputf + header_ + ".bgsubyp.csv", "w") 472 + rna = open(biorseoDir + "/" + tempDir + header_ + ".bgsubyp.csv", "w")
652 rna.write("Motif,Score,Start1,End1,Start2,End2...\n") 473 rna.write("Motif,Score,Start1,End1,Start2,End2...\n")
653 for i, module in enumerate(insertion_sites): 474 for i, module in enumerate(insertion_sites):
654 if len(module): 475 if len(module):
...@@ -687,8 +508,8 @@ class BiorseoInstance: ...@@ -687,8 +508,8 @@ class BiorseoInstance:
687 except: 508 except:
688 r = 1 509 r = 1
689 pass 510 pass
690 - if r: 511 + # if r:
691 - fails.append(j) 512 + # fails.append(j)
692 running_stats[1] += 1 513 running_stats[1] += 1
693 return r 514 return r
694 515
...@@ -729,48 +550,12 @@ class BiorseoInstance: ...@@ -729,48 +550,12 @@ class BiorseoInstance:
729 print("Computations ran successfully.") 550 print("Computations ran successfully.")
730 print() 551 print()
731 552
732 - def check_result_existence(self, datatype, method, function, with_PK, basename):
733 - folder = self.outputf+"PK/" if with_PK else self.outputf+"noPK/"
734 - if datatype == "bgsu":
735 - if method == "jar3d":
736 - extension = ".jar3d"
737 - elif method == "byp":
738 - extension = ".bgsubyp"
739 - else:
740 - raise "Unknown method !"
741 - elif datatype == "desc":
742 - if method == "dpm":
743 - extension = ".raw"
744 - elif method == "byp":
745 - extension = ".byp"
746 - else:
747 - raise "Unknown method !"
748 - else:
749 - raise "Unknown data type !"
750 - return path.isfile(folder + basename + extension + function)
751 -
752 - def check_csv_existence(self, datatype, method, basename):
753 - if datatype == "bgsu":
754 - if method == "jar3d":
755 - extension = ".sites.csv"
756 - elif method == "byp":
757 - extension = ".bgsubyp.csv"
758 - else:
759 - raise "Unknown method !"
760 - elif datatype == "desc":
761 - if method == "byp":
762 - extension = ".byp.csv"
763 - else:
764 - raise "You cannot use " + method + " with " + datatype + " data !"
765 - else:
766 - raise "Unknown data type !"
767 - return path.isfile(self.outputf + basename + extension)
768 -
769 def list_jobs(self): 553 def list_jobs(self):
770 554
771 # Read fasta file, which can contain one or several RNAs 555 # Read fasta file, which can contain one or several RNAs
772 RNAcontainer = [] 556 RNAcontainer = []
773 subprocess.call(["mkdir", "-p", self.outputf]) # Create the output folder 557 subprocess.call(["mkdir", "-p", self.outputf]) # Create the output folder
558 + subprocess.call(["mkdir", "-p", tempDir]) # Create the temp folder
774 print("loading file %s..." % self.inputfile) 559 print("loading file %s..." % self.inputfile)
775 db = open(self.inputfile, "r") 560 db = open(self.inputfile, "r")
776 c = 0 561 c = 0
...@@ -789,10 +574,10 @@ class BiorseoInstance: ...@@ -789,10 +574,10 @@ class BiorseoInstance:
789 if c == 0: 574 if c == 0:
790 seq = l[:-1].upper() 575 seq = l[:-1].upper()
791 if is_canonical_nts(seq): 576 if is_canonical_nts(seq):
792 - header = header.replace('/', '_').replace('\'','').replace('(','').replace(')','').replace(' ','_') 577 + header = header.replace('/', '_').replace('\'','').replace('(','').replace(')','').replace(' ','_').replace('>','')
793 RNAcontainer.append(RNA(header, seq)) 578 RNAcontainer.append(RNA(header, seq))
794 - if not path.isfile(self.outputf + header + ".fa"): 579 + if not path.isfile(tempDir + header + ".fa"):
795 - rna = open(self.outputf + header + ".fa", "w") 580 + rna = open(tempDir + header + ".fa", "w")
796 rna.write(">" + header +'\n') 581 rna.write(">" + header +'\n')
797 rna.write(seq +'\n') 582 rna.write(seq +'\n')
798 rna.close() 583 rna.close()
...@@ -807,7 +592,7 @@ class BiorseoInstance: ...@@ -807,7 +592,7 @@ class BiorseoInstance:
807 for instance in RNAcontainer: 592 for instance in RNAcontainer:
808 593
809 executable = biorseoDir + "/bin/biorseo" 594 executable = biorseoDir + "/bin/biorseo"
810 - fastafile = self.outputf+instance.header+".fa" 595 + fastafile = tempDir+instance.header+".fa"
811 method_type = "" 596 method_type = ""
812 ext = ".raw" 597 ext = ".raw"
813 priority = 1 598 priority = 1
...@@ -815,11 +600,11 @@ class BiorseoInstance: ...@@ -815,11 +600,11 @@ class BiorseoInstance:
815 if self.type == "jar3d": 600 if self.type == "jar3d":
816 ext = ".jar3d" 601 ext = ".jar3d"
817 method_type = "--jar3dcsv" 602 method_type = "--jar3dcsv"
818 - csv = self.outputf + instance.header + ".sites.csv" 603 + csv = tempDir + instance.header + ".sites.csv"
819 604
820 # RNAsubopt 605 # RNAsubopt
821 self.joblist.append(Job(command=["RNAsubopt", "-i", fastafile, "--outfile="+ instance.header + ".subopt"], priority=1)) 606 self.joblist.append(Job(command=["RNAsubopt", "-i", fastafile, "--outfile="+ instance.header + ".subopt"], priority=1))
822 - self.joblist.append(Job(command=["mv", instance.header + ".subopt", self.outputf], priority=2)) 607 + self.joblist.append(Job(command=["mv", instance.header + ".subopt", tempDir], priority=2))
823 # JAR3D 608 # JAR3D
824 self.joblist.append(Job(function=self.launch_JAR3D, args=[instance.seq_, instance.header], priority=3, how_many_in_parallel=1)) 609 self.joblist.append(Job(function=self.launch_JAR3D, args=[instance.seq_, instance.header], priority=3, how_many_in_parallel=1))
825 priority = 4 610 priority = 4
...@@ -827,11 +612,11 @@ class BiorseoInstance: ...@@ -827,11 +612,11 @@ class BiorseoInstance:
827 method_type = "--bayespaircsv" 612 method_type = "--bayespaircsv"
828 if self.modules == "desc": 613 if self.modules == "desc":
829 ext = ".byp" 614 ext = ".byp"
830 - csv = self.outputf + instance.header + ".byp.csv" 615 + csv = tempDir + instance.header + ".byp.csv"
831 self.joblist.append(Job(function=self.launch_BayesPairing, args=["rna3dmotif", instance.seq_, instance.header], how_many_in_parallel=-1, priority=1)) 616 self.joblist.append(Job(function=self.launch_BayesPairing, args=["rna3dmotif", instance.seq_, instance.header], how_many_in_parallel=-1, priority=1))
832 elif self.modules == "bgsu": 617 elif self.modules == "bgsu":
833 ext = ".bgsubyp" 618 ext = ".bgsubyp"
834 - csv = self.outputf + instance.header + ".bgsubyp.csv" 619 + csv = tempDir + instance.header + ".bgsubyp.csv"
835 self.joblist.append(Job(function=self.launch_BayesPairing, args=["3dmotifatlas", instance.seq_, instance.header], how_many_in_parallel=-1, priority=1)) 620 self.joblist.append(Job(function=self.launch_BayesPairing, args=["3dmotifatlas", instance.seq_, instance.header], how_many_in_parallel=-1, priority=1))
836 priority = 2 621 priority = 2
837 if self.type == "dpm": 622 if self.type == "dpm":
......